RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BcTr0k/RM_80997.SunJun301551592024 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1719787917 Database = /dev/shm/rModeler.BcTr0k/GCF_903798145.1_fDanAes4.1 - Sequences = 342 - Bases = 1381485597 - N50 = 56436977 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 69622779-74595647 | [ 2 ] 64649911-69622778 | [ ] 59677044-64649911 | [ 5 ] 54704176-59677043 | [ 6 ] 49731309-54704176 | [ 5 ] 44758441-49731308 | [ 4 ] 39785573-44758440 | [ 1 ] 34812706-39785573 | [ 2 ] 29839838-34812705 | [ ] 24866971-29839838 | [ ] 19894103-24866970 | [ ] 14921235-19894102 | [ ] 9948368-14921235 | [ ] 4975500-9948367 | [ ] 2633-4975500 |************************************************** [ 317 ] Storage Throughput = excellent ( 1475.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40566097 bp ( 40018764 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:58 (hh:mm:ss) Elapsed Time Round Time: 00:20:30 (hh:mm:ss) Elapsed Time : 1102 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23194 repeats masked totaling 4266486 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10120281 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10005539 bp After Masking: 5238202 bp Masked: 47.65 % -- Input Database Coverage: 10120281 bp out of 1381485597 bp ( 0.73 % ) Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:39 (hh:mm:ss) Elapsed Time, 7413 HSPs Collected Number of families returned by RECON: 1228 Round Time: 00:07:43 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 71207 repeats masked totaling 13208663 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30445804 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30013213 bp After Masking: 15035921 bp Masked: 49.90 % -- Input Database Coverage: 40566085 bp out of 1381485597 bp ( 2.94 % ) Sampling Time: 00:05:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:23:56 (hh:mm:ss) Elapsed Time, 46677 HSPs Collected Number of families returned by RECON: 4039 Round Time: 00:30:48 (hh:mm:ss) Elapsed Time : 143 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 221786 repeats masked totaling 40368186 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91065660 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 90026302 bp After Masking: 44333963 bp Masked: 50.75 % -- Input Database Coverage: 131631745 bp out of 1381485597 bp ( 9.53 % ) Sampling Time: 00:16:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2614041 Comparison Time: 02:39:57 (hh:mm:ss) Elapsed Time, 284741 HSPs Collected Number of families returned by RECON: 11618 Round Time: 03:03:27 (hh:mm:ss) Elapsed Time : 590 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:35:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 735546 repeats masked totaling 135202570 bp(s). - TE Masking time 00:09:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273672612 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 270013286 bp After Masking: 119046286 bp Masked: 55.91 % -- Input Database Coverage: 405304357 bp out of 1381485597 bp ( 29.34 % ) Sampling Time: 00:50:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23615628 Comparison Time: 13:37:34 (hh:mm:ss) Elapsed Time, 683525 HSPs Collected Number of families returned by RECON: 33622 Round Time: 15:02:01 (hh:mm:ss) Elapsed Time : 1236 families discovered. RepeatScout/RECON discovery complete: 3086 families found Classification Time: 01:23:12 (hh:mm:ss) Elapsed Time Program Time: 20:27:41 (hh:mm:ss) Elapsed Time